.TH g_nmeig 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_nmeig - diagonalizes the Hessian 

.B VERSION 4.5
.SH SYNOPSIS
\f3g_nmeig\fP
.BI "\-f" " hessian.mtx "
.BI "\-s" " topol.tpr "
.BI "\-of" " eigenfreq.xvg "
.BI "\-ol" " eigenval.xvg "
.BI "\-v" " eigenvec.trr "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-xvg" " enum "
.BI "\-[no]m" ""
.BI "\-first" " int "
.BI "\-last" " int "
.SH DESCRIPTION
\&g_nmeig calculates the eigenvectors/values of a (Hessian) matrix,
\&which can be calculated with \fB mdrun\fR.
\&The eigenvectors are written to a trajectory file (\fB \-v\fR).
\&The structure is written first with t=0. The eigenvectors
\&are written as frames with the eigenvector number as timestamp.
\&The eigenvectors can be analyzed with \fB g_anaeig\fR.
\&An ensemble of structures can be generated from the eigenvectors with
\&\fB g_nmens\fR. When mass weighting is used, the generated eigenvectors
\&will be scaled back to plain cartesian coordinates before generating the
\&output \- in this case they will no longer be exactly orthogonal in the
\&standard cartesian norm (But in the mass weighted norm they would be).
.SH FILES
.BI "\-f" " hessian.mtx" 
.B Input
 Hessian matrix 

.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-of" " eigenfreq.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-ol" " eigenval.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-v" " eigenvec.trr" 
.B Output
 Full precision trajectory: trr trj cpt 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]m"  "yes   "
 Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis

.BI "\-first"  " int" " 1" 
 First eigenvector to write away

.BI "\-last"  " int" " 50" 
 Last eigenvector to write away

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
